BioNetGen 2.2: Advances in Rule-Based Modeling

2015/07/31 by Leonard A. Harris, Justin S. Hogg, Jose-Juan Tapia +7 · 1 citation
Biochemistry, Genetics and Molecular Biology · #q-bio.MN #q-bio.QM

paper · pdf · doi:10.1093/bioinformatics/btw469

published as Bioinformatics 32, 3366-3368 (2016) · 3 pages, 1 figure, 1 supplementary text file. Supplementary text includes a brief discussion of the RK-PLA along with a performance analysis, two tables listing all new actions/arguments added in BioNetGen 2.2, and the "BioNetGen Quick Reference Guide". Accepted for publication in Bioinformatics

arxiv created 2016/07/01 · arxiv updated 2016/11/21

Abstract

BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discussing how they facilitate the construction, simulation, and analysis of larger and more complex models than previously possible.

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